[2024-01-24 12:21:36,166] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:36,168] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:36,168] [INFO] DQC Reference Directory: /var/lib/cwl/stg356b82fb-7de9-43d8-806c-0ecf49c1ccde/dqc_reference
[2024-01-24 12:21:37,395] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:37,396] [INFO] Task started: Prodigal
[2024-01-24 12:21:37,397] [INFO] Running command: gunzip -c /var/lib/cwl/stgb27090fd-18bc-4cae-a9ec-f5a477eaff82/GCF_000429245.1_ASM42924v1_genomic.fna.gz | prodigal -d GCF_000429245.1_ASM42924v1_genomic.fna/cds.fna -a GCF_000429245.1_ASM42924v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:44,755] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:44,755] [INFO] Task started: HMMsearch
[2024-01-24 12:21:44,755] [INFO] Running command: hmmsearch --tblout GCF_000429245.1_ASM42924v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg356b82fb-7de9-43d8-806c-0ecf49c1ccde/dqc_reference/reference_markers.hmm GCF_000429245.1_ASM42924v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:45,016] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:45,017] [INFO] Found 6/6 markers.
[2024-01-24 12:21:45,042] [INFO] Query marker FASTA was written to GCF_000429245.1_ASM42924v1_genomic.fna/markers.fasta
[2024-01-24 12:21:45,042] [INFO] Task started: Blastn
[2024-01-24 12:21:45,042] [INFO] Running command: blastn -query GCF_000429245.1_ASM42924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg356b82fb-7de9-43d8-806c-0ecf49c1ccde/dqc_reference/reference_markers.fasta -out GCF_000429245.1_ASM42924v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:46,060] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:46,064] [INFO] Selected 24 target genomes.
[2024-01-24 12:21:46,064] [INFO] Target genome list was writen to GCF_000429245.1_ASM42924v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:46,148] [INFO] Task started: fastANI
[2024-01-24 12:21:46,149] [INFO] Running command: fastANI --query /var/lib/cwl/stgb27090fd-18bc-4cae-a9ec-f5a477eaff82/GCF_000429245.1_ASM42924v1_genomic.fna.gz --refList GCF_000429245.1_ASM42924v1_genomic.fna/target_genomes.txt --output GCF_000429245.1_ASM42924v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:21:58,546] [INFO] Task succeeded: fastANI
[2024-01-24 12:21:58,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg356b82fb-7de9-43d8-806c-0ecf49c1ccde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:21:58,547] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg356b82fb-7de9-43d8-806c-0ecf49c1ccde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:21:58,569] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:21:58,569] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:21:58,569] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Schaalia meyeri	strain=FDAARGOS_985	GCA_016127995.1	52773	52773	type	True	81.2176	351	820	95	below_threshold
Schaalia meyeri	strain=DSM 20733	GCA_900105015.1	52773	52773	type	True	81.1206	347	820	95	below_threshold
Schaalia hyovaginalis	strain=DSM 10695	GCA_014208035.1	29316	29316	type	True	79.2021	301	820	95	below_threshold
Actinomyces provencensis	strain=SN12	GCA_900155435.1	1720198	1720198	type	True	78.7678	259	820	95	below_threshold
Actinomyces polynesiensis	strain=MS2	GCA_000820725.1	1325934	1325934	type	True	78.6624	243	820	95	below_threshold
Actinomyces oris	strain=FDAARGOS_1051	GCA_016127955.1	544580	544580	suspected-type	True	78.3837	198	820	95	below_threshold
Actinomyces oris	strain=CCUG 34288	GCA_006546825.1	544580	544580	suspected-type	True	78.3691	197	820	95	below_threshold
Actinomyces naeslundii	strain=Howell 279	GCA_000285995.1	1655	1655	type	True	78.3107	193	820	95	below_threshold
Actinomyces naeslundii	strain=NCTC 10301	GCA_001956585.1	1655	1655	type	True	78.2909	205	820	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	78.2609	232	820	95	below_threshold
Actinomyces dentalis	strain=DSM 19115	GCA_000429225.1	272548	272548	type	True	78.259	251	820	95	below_threshold
Actinomyces israelii	strain=DSM 43320	GCA_000711965.1	1659	1659	type	True	78.2393	232	820	95	below_threshold
Actinomyces ruminicola	strain=DSM 27982	GCA_900103885.1	332524	332524	type	True	78.1674	202	820	95	below_threshold
Actinomyces slackii	strain=ATCC 49928	GCA_000428685.1	52774	52774	type	True	78.1657	202	820	95	below_threshold
Actinomyces slackii	strain=NCTC11923	GCA_900637295.1	52774	52774	type	True	78.1226	204	820	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.5649	168	820	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	77.136	206	820	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	77.1272	189	820	95	below_threshold
Georgenia muralis	strain=DSM 14418	GCA_003814705.1	154117	154117	type	True	77.0761	193	820	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	76.7213	170	820	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	76.7078	172	820	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.5394	187	820	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.4509	152	820	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	76.2224	102	820	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:21:58,571] [INFO] DFAST Taxonomy check result was written to GCF_000429245.1_ASM42924v1_genomic.fna/tc_result.tsv
[2024-01-24 12:21:58,571] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:21:58,571] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:21:58,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg356b82fb-7de9-43d8-806c-0ecf49c1ccde/dqc_reference/checkm_data
[2024-01-24 12:21:58,572] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:21:58,610] [INFO] Task started: CheckM
[2024-01-24 12:21:58,611] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429245.1_ASM42924v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429245.1_ASM42924v1_genomic.fna/checkm_input GCF_000429245.1_ASM42924v1_genomic.fna/checkm_result
[2024-01-24 12:22:24,654] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:24,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:24,680] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:24,680] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:24,681] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429245.1_ASM42924v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:24,681] [INFO] Task started: Blastn
[2024-01-24 12:22:24,681] [INFO] Running command: blastn -query GCF_000429245.1_ASM42924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg356b82fb-7de9-43d8-806c-0ecf49c1ccde/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429245.1_ASM42924v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:26,270] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:26,275] [INFO] Selected 14 target genomes.
[2024-01-24 12:22:26,275] [INFO] Target genome list was writen to GCF_000429245.1_ASM42924v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:26,296] [INFO] Task started: fastANI
[2024-01-24 12:22:26,296] [INFO] Running command: fastANI --query /var/lib/cwl/stgb27090fd-18bc-4cae-a9ec-f5a477eaff82/GCF_000429245.1_ASM42924v1_genomic.fna.gz --refList GCF_000429245.1_ASM42924v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429245.1_ASM42924v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:32,918] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:32,934] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:32,934] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000429245.1	s__Pauljensenia georgiae	100.0	818	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.90	96.98	0.94	0.93	3	conclusive
GCF_001746855.1	s__Pauljensenia hongkongensis	93.7093	596	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	98.51	97.69	0.81	0.72	5	-
GCA_018382595.1	s__Pauljensenia sp018382595	80.7385	342	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001064145.1	s__Pauljensenia sp001064145	80.6724	375	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000185285.1	s__Pauljensenia sp000185285	80.6161	395	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.02	95.63	0.93	0.91	5	-
GCA_001072465.1	s__Pauljensenia sp001072465	80.5508	398	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.78	97.78	0.94	0.94	2	-
GCF_000466265.1	s__Pauljensenia sp000466265	80.5047	394	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.80	96.80	0.90	0.90	2	-
GCA_902373545.1	s__Pauljensenia sp902373545	80.4961	321	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.43	97.43	0.84	0.84	2	-
GCA_018375675.1	s__Pauljensenia sp018375675	80.3416	381	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847525.1	s__Pauljensenia odontolytica_B	80.2547	393	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.06	96.22	0.94	0.92	3	-
GCA_902373435.1	s__Pauljensenia sp902373435	80.112	330	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	95.35	95.27	0.85	0.81	3	-
GCF_900499005.1	s__Pauljensenia culturomici	79.7362	347	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014208035.1	s__Pauljensenia hyovaginalis	79.1997	300	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	95.48	95.48	0.88	0.88	2	-
GCA_900556405.1	s__Pauljensenia sp900556405	78.9377	235	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:32,936] [INFO] GTDB search result was written to GCF_000429245.1_ASM42924v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:32,937] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:32,941] [INFO] DFAST_QC result json was written to GCF_000429245.1_ASM42924v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:32,941] [INFO] DFAST_QC completed!
[2024-01-24 12:22:32,941] [INFO] Total running time: 0h0m57s